Somewhere I have read we share more than 99% of our genes with every other other person and 98% of our genes with chimpanzees. What does this mean? Don't we share 50% of our genes with our mother and 50% with our father?

4 Answers
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There is a distinct difference between the 'genes' that we share, and the genetic code (the DNA) that the genes are made of.

All humans (excluding genetic disorders) have the same genes, but not everyone has exactly the same code - there are tiny differences between individuals, and these are manifested in the different traits you can observe between people (eye colour, height, etc).

So you therefore have 100% of the genes that your mother has.

However, as stated in the first answer, you inherit the different 'alleles', or versions, of the genes from your parents, and end up with ~50% of the alleles from each parents (but all the genes).

With regard to species differences; many of the genes we inherit have evolved over millions (in fact billions) of years, and thus many of our genes are present in most other organisms (but in very different forms - the code/DNA). Chimpanzees are our closest relatives in evolutionary terms, and thus their genes are very similar to ours in the code (~98% the same). But this only applies to the coding regions! Less than 2% of your genome actually codes for genes - the rest is mostly regulatory (not junk, as it used to be called), and this is where the true inter-species variation lies. So whilst we have ~98% homology in the protein-coding regions, this is MUCH less if you count the whole genome.

Nice answer, +1. Actually, recent analysis of 1000 Genomes data shows that each person has some 25-40 homozygous LOF (loss of function) variants not found in either parent. Thus, one could lower the 100% figure to ~99.9% shared.
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Larry_ParnellApr 26 '12 at 15:07

How many kinds of genes are there in humans? If we all have same kind of genes, so is it just the combination of these genes that affect our personality?
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cpxApr 26 '12 at 15:35

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+1 but you should probably change the word "code" for something else. The great majority of the species on Earth use the same genetic code (I do understand you did not mean it like that but...)
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nicoApr 26 '12 at 17:48

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@user103431 I think there are around 23,000 accepted protein-coding genes in humans. We each have a copy of every gene. But at the DNA level the genes can vary ever so slightly, and this is where the different alleles come from (slight variations in the same trait). With regard to your personality, that is another kettle of fish: your genes can certainly affect your predisposition to certain mentalities, but it should be fairly clear that it is your life experiences that mostly affect how you develop, and thus what kind of person you become. And 'code' is a bit layman, but it is 'correct'
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LukeApr 27 '12 at 15:40

Also, the DNA formerly known as junk is called heterochromatin. This was long thought to be inactive but I believe that is has now been shown to contain protein coding genes, not just regulatory elements (I spoke to Gary Karpen in the summer and think this is where I heard it). It is quite an unknown entity because it is so damned hard to sequence thanks to lots of repeating units!
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GriffinEvoNov 15 '12 at 16:02

In every cell of your body, you have two physical copies of every gene (ignoring gametes, / copy number variations), one from your mother, one from your father. (Humans are diploid.) That's why it's correct to say that you got 50% from either parent (ignoring the 13 mitochondrial genes that are inherited from the mother only).

The second approach is to look at genes as abstract entities. In the abstract sense, you share 100% of your genes with fellow humans, and more distant species will have a number of different genes. (This difference can be quantified in many different ways.)

Let's not forget in these explanations about the special case of X and Y genes. If you are a boy, you share 100% of your father's Y chromosome (with a few mutations/transcriptions errors and slight recombinations in between) and a 50% mix of a X chromosome from him and a X chromosome from your mother.
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ogerardJun 7 '12 at 14:26

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@ogerard: Boys get one complete Y chromosome from the father, and one complete X chromosome from the mother. (The sperm was carrying a Y, and not an X.) Girls get one X from each of their parents. (So no 50/50 mix in the X for boys.)
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Michael KuhnJun 8 '12 at 5:54

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@Michael Kuhn: Sorry, I was really not correct in the end part of my comment. What I should have written is that the X from their mother is a recombination of the two Xs of their mother. There is a small recombinable part in the Y chromosome but it does not contain the key genes for sex determination.
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ogerardJun 8 '12 at 8:56

Say x is the percentage of an allele in your mom (or cousin, or brother). Say c is the filial similarity (brother=.5, son=.5, cousins=.125, etc.) of the allele. Say y is the general probability of having that allele in that population (assuming mom is the same species with you). Say f(x,y) is the expected value of the number of allele that you have.

Then f(x,y)= c * x+ (1-c) *y

In other word. There is no contradiction in the idea that we are 98% similar with monkeys and yet only 50% similar with our own mom.

Here, the world similar is used in totally different sense.

f(x,y) is 99% for most allele. Now let gy(x)=f(x,y) then

gy'(x) is c.

In other word, for every allele your mom have, it'll improve the expected value of you having the same allele by half. For each allele your cousin has, it'll improve the expected value of you having the same allele by 1/8th. That is for the same y. For most y, similarity is 100% nevertheless.

Say Ann, Beth, and Cindy has AA, Aa, and aa alleles.

Then Ann's sons have 25% higher expected value of having A alleles than Beth, and Beth have 25% higher expected value of having A alleles than Cindy. I say nothing of actual probability distribution.

Ann's cousins have .0625% higher expected value of A occurrence than Beth's cousins and .125% expected value of A occurrence than Cindy's cousins

Disclaimer: We do not take into account that people mate with those who are genetically similar but not too similar (i.e. no inbreeding).

Another way to see this is to look at y. For rare genes y is small. Hence.

50-50 is for genes that are rare and family specific. If your mother is color blind (100% carrier), the expected value of the number of color blind carrier is improved by 50%. It doesn't mean you'll be color blind. We'll have to go to the technicality of dominant vs recessive. But that's the idea.

For genes that are NOT rare, say genes that make you have 2 feet and 2 hand, you still share all your mom's genes. That's because everybody have that. Your mom have that, and your dad have that, and so is everyone else, including chimps.

Is this what most directly answer your question?

Again the issue is rarity. For rare genes P(You have it|mom have it) is 50%.

For common genes,

P(You have it|mom have it) = P(You have it and mom have it)/P(mom have it). //By bayesian rule